Professor

School of Basic Medical Sciences

Southern Medical University

present - 2018

• Associate director， Department of Bioinformatics

Post-doctoral Fellow

State Key Laboratory of Infectious Diseases

The University of Hong Kong

2018 - 2017

Bioinformatician

Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes

Jinan University

2013 - 2009

PhD., Bioinformaitcs

The University of Hong Kong

Hong Kong, CN

2017 - 2013

• Thesis: Big-data computational methods for studying molecular evolution: from accurate genome assembly to phylogenetic analysis and data integration

M.S., Biochemistry and Molecular Biology

Anhui Medical University

Hefei, CN

2009 - 2006

• Thesis: miRNA靶基因<U+8BA1>算分析新方法及其<U+5E94>用研究

B.S., Biotechnology

South China Agricultural University

Guangzhou, CN

2005 - 2001

南方<U+533B>科大<U+5B66>高<U+5C42>次人才“不忘初心 牢<U+8BB0>使命”<U+5B66><U+4E60>教育

延安干部培<U+8BAD><U+5B66>院

Yan’an, CN

2018

Train the Trainers

Institut Pasteur

Paris, FR

2015

Certificate of Teaching and Learning in Higher Education

Centre for Enhancement of Teaching and Learning

The University of Hong Kong

2015

BMB209: Workshops in Applied Bioinformatics

Department of Biochemistry and Molecular Biology

University of Southern Denmark

2019

• PhD level class, invited lecture

生物信息<U+5B66>科研<U+8BAD><U+7EC3>

School of Basic Medical Sciences

Southern Medical University

• Undergraduate level class

基因<U+7EC4><U+5B66>

School of Basic Medical Sciences

Southern Medical University

• Undergraduate level class

基<U+7840><U+533B><U+5B66>新<U+8FDB>展<U+8BB2>座

School of Basic Medical Sciences

Southern Medical University

• Undergraduate level class

功能蛋白<U+8D28>研究

College of Life Science and Technology

Jinan University

2012 - 2011

• Graduate level class

南方<U+533B>科大<U+5B66>第三<U+5C42>次人才引<U+8FDB>科研<U+9879>目 (G618289088)

PI, CNY ￥1,500,000

N/A

2020 - 2018

hnRNPK蛋白在<U+8C03>控人肺癌<U+7EC6>胞周期胞<U+8D28>分裂中的作用研究 (21613414)

PI, CNY ￥100,000, 中央高校基本科研<U+4E1A><U+52A1><U+8D39><U+4E13><U+9879><U+8D44>金

N/A

2013

Hela<U+7EC6>胞周期<U+52A8><U+6001>蛋白<U+8D28><U+7EC4><U+5B66>分析 (21611303)

PI, CNY ￥20,000, 中央高校基本科研<U+4E1A><U+52A1><U+8D39><U+4E13><U+9879><U+8D44>金

N/A

2011

生物信息<U+5B66>II

《功能蛋白<U+8D28>研究》. 385-425. 何<U+5E86>瑜（主<U+7F16>），科<U+5B66>出版社 (“十二五”<U+56FD>家重<U+70B9><U+56FE><U+4E66>出版<U+89C4>划<U+9879>目)

N/A

2012

• 余光<U+521B>

treeio: an R package for phylogenetic tree input and output with richly annotated and associated data

Molecular Biology and Evolution. 2019, accepted

N/A

2019

• LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu^*
• Impact Factor = 14.797

Two methods for mapping and visualizing associated data on phylogeny using ggtree¹

Molecular Biology and Evolution. 2018, 35(12):3041-3043.

N/A

2018

• G Yu^*, TTY Lam, H Zhu, Y Guan^*
• Impact Factor = 14.797

Using meshes for MeSH term enrichment and semantic analyses²

Bioinformatics. 2018, 34(21):3766–3767.

N/A

• G Yu

ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data³

Methods in Ecology and Evolution. 2017, 8(1):28-36

N/A

2017

• G Yu, DK Smith, H Zhu, Y Guan, TTY Lam^*
• ESI Highly Cited Paper

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization⁴

Molecular BioSystems. 2016, 12(2):477-479

N/A

2016

• G Yu, QY He^*
• ESI Highly Cited Paper

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae⁵

Frontiers in Microbiology. 2016, 7:78

N/A

• XY Yang, K He, G Du, X Wu, G Yu, Y Pan, G Zhang^*, X Sun^*, QY He^*

Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015⁶

Infection, Genetics and Evolution. 2016, 38:96-100

N/A

• PY Huang, CCD Lee, CH Yip, CL Cheung, G Yu, TTY Lam, DK Smith, H Zhu^*, Y Guan^*

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization⁷

Bioinformatics. 2015, 31(14):2382-2383

N/A

2015

• G Yu^*, LG Wang, QY He^*
• ESI Highly Cited Paper

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis⁸

Bioinformatics. 2015, 31(4):608-609

N/A

• G Yu^*, LG Wang, GR Yan, QY He^*

ACK1 Promotes Gastric Cancer Epithelial-Mesenchymal Transition and Metastasis through AKT-POU2F1-ECD Signaling⁹

Journal of Pathology. 2015, 236(2):175-185

N/A

• SH Xu, JZ Huang, ML Xu, G Yu, XF Yin, D Chen^*, GR Yan^*

Proteomic analysis on the copper resistance of Streptococcus pneumonia¹⁰

Metallomics. 2015, 7(3):448-454

N/A

• Z Guo, J Han, XY Yang, K Cao, K He, G Du, G Zeng, L Zhang, G Yu, Z Sun, QY He^*, X Sun^*

Proteomic analysis on the antibacterial activity of a Ru(II) complex against Strepococcus pneumonia¹¹

Journal of Proteomics. 2015, 115:107-116

N/A

• XY Yang, L Zhang, J Liu, N Li, G Yu, K Cao, J Han, G Zeng, Y Pan, X Sun^*, QY He^*

Proteomic analysis of putative heme-binding proteins in Streptococcus pyogenes¹²

Metallomics. 2014, 6(8):1451-1459

N/A

2014

• N Wang^#, J Zhang^#, L Zhang, XY Yang, N Li, G Yu, J Han, K Cao, Z Guo, X Sun^*, QY He^*

Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumonia¹³

Metallomics. 2013, 5(7):928-935

N/A

2013

• X Sun^#, G Yu^#, Q Xu, N Li, C Xiao, X Yin, K Cao, J Han, QY He^*

A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism¹⁴

Proteomics, 2013, 13(1):169-178

N/A

• YY Zhu^#, G Yu^#, Y Zhang, Z Xu, YQ Huang, GR Yan^*, QY He^*

A DNA-Based Semantic Fusion Model for Remote Sensing Data¹⁵

PLoS One. 2013, 8(10):e77090

N/A

• H Sun^*, J Weng, G Yu, RH Massawe

Quantitative Proteomics Characterization on the Anti-tumor Effects of Isodexyelephantopin against Nasopharyngeal Carcinoma¹⁶

Proteomics. 2013, 13(21):3222-3232

N/A

• GR Yan^#, Z Tan^#, Y Wang, ML Xu, G Yu, Y Li^*, QY He^*

Design, SAR, angiogenic activities evaluation and pro-angiogenic mechanism of new marine cyclopeptide analogs¹⁷

Current Medicinal Chemistry. 2013, 20(9):1183-1194

N/A

• J Li, X Lu, Q Wu, G Yu, Z Xu, L Qiu, Z Pei, Y Lin, J Pang^*

Proteomic investigation of the interactome of FMNL1 in hematopoietic cells unveils a role in calcium-dependent membrane plasticity¹⁸

Journal of Proteomics. 2013, 78:72-82

N/A

• Y Han, G Yu, H Sarioglu, A Caballero-Martinez, F Schlott, M Ueffing, H Haase, C Peschel, AM Krackhardt^*

LXtoo: an integrated live Linux distribution for the bioinformatics community¹⁹

BMC Research Notes. 2012, 5(1):360

N/A

2012

• G Yu^#, LG Wang^#, XH Meng, QY He^*

clusterProfiler: an R package for comparing biological themes among gene clusters²⁰

OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287

N/A

• G Yu, LG Wang, Y Han, QY He^*
• ESI Highly Cited Paper

Cellular MicroRNA let-7c Inhibits M1 Protein Expression of the H1N1 Influenza A Virus in Infected Human Lung Epithelial Cells²¹

Journal of Cellular and Molecular Medicine. 2012, 16(10):2539-2546

N/A

• Y Ma^#, J Yang^#, X Fan^#, H Zhao, W Hu, Z Li, G Yu, X Ding, J Wang, X Bo, X Zheng, Z Zhou^*, S Wang^*

Genistein-induced mitotic arrest of gastric cancer cells by downregulating KIF20A, a proteomics study²²

Proteomics. 2012, 12(14):2391-2399

N/A

• GR Yan^#, FY Zhou^#, BL Dang, Y Zhang, G Yu, X Liu, QY He^*

Functional similarity analysis of human virus-encoded miRNAs²³

Journal of Clinical Bioinformatics. 2011, 1(1):15

N/A

2011

• G Yu, QY He^*

A new method for measuring functional similarity of microRNAs²⁴

Journal of Integrated OMICS. 2011, 1(1):49-54

N/A

• G Yu^#, CL Xiao^#, X Bo, CH Lu, Y Qin, S Zhan, QY He^*

Phosphoproteome profile of human lung cancer cell line A549²⁵

Molecular BioSystems. 2011, 7(2):472-479

N/A

• G Yu^#, CL Xiao^#, CH Lu^#, HT Jia, F Ge, W Wang, XF Yin, HL Jia, JX He^*, QY He^*

Proteomic Analysis of Membrane Proteins from Streptococcus pneumoniae with Multiple Separation Methods plus High Accuracy Mass Spectrometry²⁶

OMICS: A Journal of Integrative Biology. 2011, 15(10):683-694

N/A

• X Sun^#, XY Yang^#, XF Yin, G Yu, CL Xiao, X He, QY He^*

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products²⁷

Bioinformatics. 2010, 26(7):976-978

N/A

2010

• G Yu^#, F Li^#, Y Qin, X Bo^*, Y Wu, S Wang^*
• ESI Highly Cited Paper

<U+7ED3>合基因<U+7EC4>分析<U+9884><U+6D4B>炎症相<U+5173>miRNA及其靶<U+6807>

<U+519B>事<U+533B><U+5B66>科<U+5B66>院院刊. 2009, 33(3):245-247

N/A

2009

• 余光<U+521B>，王超，<U+8BB8>尹，伯<U+6653>晨，王升<U+542F>^*，秦宜德^*

依<U+8D56>于5’端非<U+7F16><U+7801><U+533A>高<U+7EA7><U+7ED3>构的真核生物mRNA翻<U+8BD1><U+8C03>控

中<U+56FD>生物化<U+5B66>与分子生物<U+5B66><U+62A5>. 2007, 23(11):881-887

N/A

2007

• 余光<U+521B>，秦宜德，伯<U+6653>晨，王升<U+542F>^*

R<U+8BED>言在生物信息<U+5B66><U+6570>据可<U+89C6>化中的<U+5E94>用

第八<U+5C4A>南方<U+533B>院博士<U+8BBA><U+575B>之《研之有信》, Oct 2019

Southern Medical University

2019

Data integration and visualization of phylogenetic trees

Managing Zoonotic Infections in the era of One Health, Oct 2019

Guangzhou Medical University

Two methods for mapping and visualizing associated data on phylogeny using ggtree

第一<U+5C4A>南方<U+533B>科大<U+5B66>基<U+7840><U+533B><U+5B66><U+5B66><U+672F>年<U+4F1A>, Jan 2019

Southern Medical University

Data integration and visualization of phylogenetic trees

The 3^rd South Lake Innovation Forum for International Young Talents, May 2018

Huazhong Agricultural University

2018

ggtree for tree visualization & annotation

Phylogenetic tree visualization workshop/hackathon, May 2017

The Field Museum of Natural History

2017

Computational Methods in Ecology and Evolution

The Second International Workshop on Environmental Microbiomes, Apr 2017

Sun Yat-sen University

ggtree for visualization and annotation of phylogenetic trees

The 9^th China-R Conference, May 2016

Renmin University of China

2016